The druggability of the ATP binding site of glycogen phosphorylase kinase probed by coumarin analogues

Glycogen phosphorylase kinase (PhK) converts by phosphorylation, the inactive glycogen phosphorylase (GPb) into active GPa in the glycogenolytic pathway. It is a complex enzyme comprising of the catalytic (γ) and three regulatory subunits (α, β, δ) forming a hexadecamer with stoichiometry (αβγδ)4. Several studies have indicated PhK as a promising target for the development of antihyperglycemics as its inhibition blocks glycogenolysis in liver and a potential therapeutic target for cancer against pathological angiogenesis and tumor progression. The identification of compounds that inhibit the kinase through their direct binding to its catalytic site is an effective approach to identify bioactive molecules of therapeutic significance. Towards this, the structure of the N-terminal kinase domain (residues 1–298) of the catalytic γ subunit of PhK (PhKγtrnc) has been determined by X-ray crystallography while staurosporine and indirubin analogues have been characterized as potent inhibitors targeting the ATP binding site. In this study, a series of 38 synthetic analogues of naturally occurring coumarins were screened for inhibition of PhKγtrnc, in vitro, using a photometric assay. The IC50 values of the two most potent compounds were determined for PhKγtrnc and the pharmacologically relevant target, human liver isoform (PHKG2A). Their cellular efficacy and toxicity in HepG2 cells were further assessed ex vivo. Docking experiments and the structural comparison with previously described inhibitors reveal the binding mode of the coumarin scaffold at a no hinge region of the ATP site of PhK and the role of a conserved β3-Lys in binding. The experimental findings provide structural insights with implications to the kinase targeting and drug design

Green Synthetic Approaches for Biologically Relevant Heterocycles

Green Synthetic Approaches for Biologically Relevant Heterocycles reviews this significant group of organic compounds within the context of sustainable methods and processes. Each clearly structured chapter features in-depth coverage of various green protocols for the synthesis of a wide variety of bioactive heterocycles classified on the basis of ring-size and/or presence of heteratoms(s). Techniques covered include microwave heating, ultrasound, ionic liquids, solid phase, solvent-free, heterogeneous catalysis, and aqueous media, along with multi-component reaction strategies. This book also integrates advances in green chemistry research into industrial applications and process developments. Green Synthetic Approaches for Biologically Relevant Heterocycles is an essential resource on green chemistry technologies for academic researchers, R & D professionals, and students working in medicinal, organic, natural product, and agricultural chemistry.Includes bibliographical references and index.Online resource; title from PDF title page (EBSCO, viewed November 20, 2014).Green Synthetic Approaches for Biologically Relevant Heterocycles reviews this significant group of organic compounds within the context of sustainable methods and processes. Each clearly structured chapter features in-depth coverage of various green protocols for the synthesis of a wide variety of bioactive heterocycles classified on the basis of ring-size and/or presence of heteratoms(s). Techniques covered include microwave heating, ultrasound, ionic liquids, solid phase, solvent-free, heterogeneous catalysis, and aqueous media, along with multi-component reaction strategies. This book also integrates advances in green chemistry research into industrial applications and process developments. Green Synthetic Approaches for Biologically Relevant Heterocycles is an essential resource on green chemistry technologies for academic researchers, R & D professionals, and students working in medicinal, organic, natural product, and agricultural chemistry.Front Cover; Green Synthetic Approaches for Biologically Relevant Heterocycles; Copyright; Dedication; Contents; Contributors; About the Editor; Foreword; Preface; Chapter 1 -- Green Synthetic Approaches for Biologically Relevant Heterocycles: An Overview; 1. INTRODUCTION; 2. AN OVERVIEW OF THE BOOK; 3. CONCLUDING REMARKS; Chapter 2 -- Synthesis of Bioactive Five- and Six-Membered Heterocycles Catalyzed by Heterogeneous Supported Metals; 1. INTRODUCTION; 2. SYNTHESIS OF N-CONTAINING HETEROCYCLES; 3. SYNTHESIS OF OXYGEN-CONTAINING HETEROCYCLES; 4. SYNTHESIS OF SULFUR-CONTAINING HETEROCYCLES.5. CONCLUDING REMARKSReferences; Chapter 3 -- Transition-Metal-Free Synthesis of Benzo-Fused Five- and Six-Membered Heterocycles Employing Arynes; 1. INTRODUCTION; 2. SYNTHESIS OF FIVE-MEMBERED HETEROCYCLES; 3. SYNTHESIS OF SIX-MEMBERED HETEROCYCLES; 4. SYNTHESIS OF MEDIUM-SIZED HETEROCYCLES; 5. APPLICATIONS OF THE BENZO-FUSED HETEROCYCLES; 6. CONCLUDING REMARKS; References; Chapter 4 -- Metal-Catalyzed Routes for the Synthesis of Furocoumarins and Coumestans; 1. INTRODUCTION; 2. SYNTHETIC ROUTES TO FUROCOUMARIN DERIVATIVES; 3. SYNTHETIC ROUTES TO COUMESTAN DERIVATIVES; 4. CONCLUDING REMARKS.AcknowledgmentsReferences; Chapter 5 -- Green Solvents for Eco-friendly Synthesis of Bioactive Heterocyclic Compounds; 1. INTRODUCTION; 2. HETEROCYCLIC SYNTHESIS IN SUPERCRITICAL CARBON DIOXIDE; 3. HETEROCYCLIC SYNTHESIS IN PEG; 4. HETEROCYCLIC SYNTHESIS IN GLYCEROL; 5. HETEROCYCLIC SYNTHESIS IN GLUCONIC ACID AQUEOUS SOLUTION; 6. HETEROCYCLIC SYNTHESIS IN ETHYL LACTATE; 7. CONCLUDING REMARKS; References; Chapter 6 -- Green Catalytic Synthesis of Heterocyclic Structures Using Carbon Dioxide and Related Motifs; 1. INTRODUCTION; 2. BIOLOGICAL IMPORTANCE OF CO2-BASED HETEROCYCLIC COMPOUNDS.3. GREEN SYNTHESIS OF 1,3-DIOXOLAN-2-ONES AND 1,3-DIOXAN-2-ONES USING CO24. GREEN SYNTHESIS OF OXAZOLIDINONES AND OXAZODINANONES USING CO2; 5. RELATED HETEROCYCLES INCORPORATING CO2 OR RELATED SYNTHONS; 6. CONCLUDING REMARKS; References; Chapter 7 -- Synthetic Approaches to Small- and Medium-Size Aza-Heterocycles in Aqueous Media; 1. INTRODUCTION; 2. THREE-MEMBERED RING-AZIRIDINES; 3. FOUR-MEMBERED RINGS; 4. FIVE-MEMBERED RINGS; 5. SIX-MEMBERED RINGS; 6. SEVEN-MEMBERED RINGS; 7. CONCLUDING REMARKS; References.CHAPTER 8 -- Green Synthetic Approaches forBiologically Relevant 2-amino-4H-pyransand 2-amino-4H-pyran-Annulated Heterocyclesin Aqueous Media1. INTRODUCTION; 2. SYNTHETIC APPROACHES FOR 2-AMINO-4H-PYRANS AND 2-AMINO-4H-PYRAN-ANNULATED HETEROCYCLES IN WATER AND ETHANOL-WATER MEDIA; 3. CONCLUDING REMARKS; Acknowledgments; References; Chapter 9 -- Sustainable Synthesis of Benzimidazoles, Quinoxalines, and Congeners; 1. INTRODUCTION; 2. METHODS OF SYNTHESIS OF BENZIMIDAZOLES/QUINOXALINES USING GREENER STRATEGIES; 3. CONCLUDING REMARKS; References.Elsevie

Biotechnology of microbial enzymes : production, biocatalysis and industrial applications /

Includes index.Print version record.Includes bibliographical references and index.Front Cover -- Biotechnology of Microbial Enzymes -- Copyright Page -- Dedication -- Contents -- List of Contributors -- Preface -- 1 Useful Microbial Enzymes-An Introduction -- 1.1 The Enzymes: A Class of Useful Biochemicals -- 1.2 Microbial Enzymes for Industry -- 1.3 Improvement of Enzymes -- 1.4 Discovery of New Enzymes -- 1.5 Concluding Remarks -- Acknowledgements -- References -- 2 Production, Purification, and Application of Microbial Enzymes -- 2.1 Introduction -- 2.2 Production of Microbial Enzymes -- 2.2.1 Enzyme Production in Industries -- 2.2.2 Industrial Enzyme Production Technology -- 2.2.2.1 Submerged Fermentation -- 2.2.2.2 Solid State Fermentation -- 2.3 Strain Improvements -- 2.3.1 Mutation -- 2.3.2 Recombinant DNA (rDNA) Technology -- 2.3.3 Protein Engineering -- 2.4 Downstream Processing/Enzyme Purification -- 2.5 Product Formulations -- 2.6 Global Enzyme Market Scenarios -- 2.7 Industrial Applications of Enzymes -- 2.7.1 Food Industry -- 2.7.1.1 Starch Industry -- 2.7.1.2 Baking Industry -- 2.7.1.3 Brewing Industry -- 2.7.1.4 Fruit Juice Industry -- 2.7.2 Textile Industry -- 2.7.3 Detergent Industry -- 2.7.4 Pulp and Paper Industry -- 2.7.5 Animal Feed Industry -- 2.7.6 Leather Industry -- 2.7.7 Biofuel From Biomass -- 2.7.8 Enzyme Applications in the Chemistry and Pharma Sectors -- 2.7.8.1 Speciality Enzymes -- 2.7.8.2 Enzymes in Personal Care Products -- 2.7.8.3 Enzymes in DNA-Technology -- 2.8 Concluding Remarks -- References -- 3 Solid State Fermentation for Production of Microbial Cellulases -- 3.1 Introduction -- 3.2 Solid State Fermentation (SSF) -- 3.2.1 Comparative Aspects of Solid State and Submerged Fermentations -- 3.2.2 Cellulase-Producing Microorganisms in SSF -- 3.2.3 Extraction of Microbial Cellulase in SSF -- 3.2.4 Measurement of Cellulase Activity in SSF -- 3.2.4.1 Filter Paper Activity (FPase).3.2.4.2 Carboxymethyl Cellulase Activity (CMCase) -- 3.2.4.3 Xylanase Activity -- 3.2.4.4 -Glucosidase Activity -- 3.3 Lignocellulosic Residues/Wastes as Solid Substrates in SSF -- 3.4 Pretreatment of Agricultural Residues -- 3.4.1 Physical/Mechanical Pretreatments -- 3.4.1.1 Mechanical Comminution -- 3.4.1.2 Grinding/Milling/Chipping -- 3.4.2 Physico-Chemical Pretreatments -- 3.4.2.1 Steam Explosion (Autohydrolysis) -- 3.4.3 Chemical Pretreatments -- 3.4.4 Biological Pretreatment -- 3.5 Environmental Factors Affecting Microbial Cellulase Production in SSF -- 3.5.1 Water Activity/Moisture Content -- 3.5.2 Temperature -- 3.5.3 Mass Transfer Processes: Aeration and Nutrient Diffusion -- 3.5.3.1 Gas Diffusion -- 3.5.3.2 Nutrient Diffusion -- 3.5.4 Substrate Particle Size -- 3.5.5 Other Factors -- 3.6 Strategies to Improve Production of Microbial Cellulase -- 3.6.1 Metabolic Engineering and Strain Improvement -- 3.6.2 Recombinant Strategy (Heterologous Cellulase Expression) -- 3.6.2.1 Yeast Expression Systems -- 3.6.2.2 Bacterial Expression Systems -- 3.6.2.3 Plant Expression System -- 3.6.3 Mixed-Culture (Coculture) Systems -- 3.7 Fermenter (Bioreactor) Design for Cellulase Production in SSF -- 3.7.1 Tray Type Bioreactor -- 3.7.2 Rotary Drum Bioreactor -- 3.7.3 Packed Bed Bioreactor -- 3.7.4 Fluidized Bed Bioreactor -- 3.8 Biomass Conversion and Application of Microbial Cellulases -- 3.8.1 Textile Industry -- 3.8.2 Laundry and Detergents -- 3.8.3 Food and Animal Feed -- 3.8.4 Pulp and Paper Industry -- 3.8.5 Biofuels -- 3.9 Concluding Remarks -- Abbreviations -- References -- 4 Hyperthermophilic Subtilisin-Like Proteases From Thermococcus kodakarensis -- 4.1 Introduction -- 4.2 Two Subtilisin-Like Serine Proteases From Thermococcus kodakarensis KOD1 -- 4.3 Tk-Subtilisin -- 4.3.1 Ca2+-Dependent Maturation of Tk-Subtilisin.4.3.2 Crystal Structures of Tk-Subtilisin -- 4.3.3 Requirement of Ca2+-Binding Loop for Folding -- 4.3.4 Ca2+ Ion Requirements for Hyperstability -- 4.3.5 Role of Tkpro -- 4.3.6 Role of the Insertion Sequences -- 4.3.7 Cold-Adapted Maturation Through Tkpro Engineering -- 4.3.8 Degradation of PrPSc by Tk-Subtilisin -- 4.3.9 Tk-Subtilisin Pulse Proteolysis Experiments -- 4.4 Tk-SP -- 4.4.1 Maturation of Pro-Tk-SP -- 4.4.2 Crystal Structure of Pro-S359A* -- 4.4.3 Role of proN -- 4.4.4 Role of the C-Domain -- 4.4.5 PrPSc Degradation by Tk-SP -- 4.5 Concluding Remarks -- Acknowledgments -- Abbreviations -- References -- 5 Enzymes from Basidiomycetes-Peculiar and Efficient Tools for Biotechnology -- 5.1 Introduction -- 5.2 Brown and White Rot Fungi -- 5.3 Isolation and Laboratory Maintenance of Wood Rot Basidiomycetes -- 5.4 Basidiomycetes as Producers of Enzymes Involved in Degradation of Lignocellulose Biomass -- 5.4.1 Enzymes Involved in the Degradation of Cellulose and Hemicelluloses -- 5.4.2 Enzymes Involved in Lignin Degradation -- 5.5 Production of Ligninolytic Enzymes by Basidiomycetes: Screening and Production in Laboratory Scale -- 5.6 General Characteristics of the Main Ligninolytic Enzymes with Potential Biotechnological Applications -- 5.6.1 Laccases -- 5.6.2 Peroxidases -- 5.7 Industrial and Biotechnological Applications of Ligninolytic Enzymes from Basidiomycetes -- 5.7.1 Application of Ligninolytic Enzymes in Delignification of Vegetal Biomass and Biological Detoxification for Biofuel P ... -- 5.7.2 Application of Ligninolytic Enzymes in the Degradation of Xenobiotic Compounds -- 5.7.3 Application of Ligninolytic Enzymes in the Degradation of Textile Dyes -- 5.7.4 Application of Ligninolytic Enzymes in Pulp and Paper Industry -- 5.8 Concluding Remarks -- Acknowledgments -- References.6 Microbial Production and Molecular Engineering of Industrial Enzymes: Challenges and Strategies -- 6.1 Introduction -- 6.2 Strategies for Achieving High-Level Expression of Industrial Enzymes in Microorganisms -- 6.2.1 Strategies for High-Level Expression of Microbial Enzymes in E. coli -- 6.2.1.1 High-Level Expression of Enzymes by Transcriptional Regulation in E. coli -- 6.2.1.2 High-Level Expression of Enzymes by Translational Regulation in E. coli -- 6.2.1.3 Enhancement of the Expression of Enzymes by Different Protein Formations in E. coli -- 6.2.1.4 Improving Enzyme Production Yield by Fusion Proteins or Molecular Chaperones in E. coli -- 6.2.1.5 High-Level Expression of Enzymes by Codon Optimization in E. coli -- 6.2.1.6 Fermentation Optimization of Enzyme Production in E. coli -- 6.2.2 High-Level Expression of Microbial Enzymes in Bacilli -- 6.2.3 High-Level Expression of Microbial Enzymes in Lactic Acid Bacteria -- 6.2.4 High-Level Expression of Microbial Enzymes in Yeasts -- 6.2.4.1 High-Level Expression of Microbial Enzymes in P. pastoris -- 6.2.4.2 High-Level Expression of Microbial Enzymes in S. cerevisiae -- 6.2.4.3 High-Level Expression of Microbial Enzymes in Other Yeast Hosts -- 6.2.5 High-Level Expression of Microbial Enzymes in Filamentous Fungi -- 6.2.5.1 High-Level Expression of Microbial Enzymes in Aspergillus Species -- 6.2.5.2 High-Level Expression of Microbial Enzymes in Trichoderma Species -- 6.2.5.3 High-Level Expression of Microbial Enzymes in Other Filamentous Fungi Species -- 6.3 Molecular Engineering Strategies -- 6.3.1 Directed Evolution -- 6.3.2 Site-Directed Mutagenesis -- 6.3.3 Saturation Mutagenesis -- 6.3.4 Truncation -- 6.3.5 Fusion -- 6.4 Concluding Remarks -- References -- 7 Metagenomics and the Search for Industrial Enzymes -- 7.1 Introduction -- 7.2 The Dilemma Between Known, Engineered, or Novel Enzymes.7.3 Metagenomics and Its Application to Enzyme Research -- 7.4 Success Stories of Naïve and Direct Sequencing Screens for New Enzymes -- 7.5 Success Stories for Introducing Environmental Enzymes into the Market -- 7.6 Enzyme Search: Limitations of Metagenomics and Solutions -- 7.7 Concluding Remarks -- Acknowledgments -- References -- 8 The Pocket Manual of Directed Evolution: Tips and Tricks -- 8.1 Introduction -- 8.2 Methods to Generate DNA Diversity -- 8.2.1 Mutagenic Methods -- 8.2.1.1 Random Mutagenesis -- 8.2.1.2 Saturation Mutagenesis -- 8.2.2 DNA Recombination Methods -- 8.2.2.1 In Vitro Methods -- 8.2.2.1.1 Homology-Dependent Recombination Methods -- 8.2.2.1.2 Homology-Independent Recombination Methods -- 8.2.2.2 In Vivo Methods -- 8.3 Computational Tools -- 8.4 Functional Expression Systems -- 8.5 Mutant Library Exploration -- 8.5.1 Genetic Selection Methods -- 8.5.2 High-Throughput Screening (HTS) Assays -- 8.5.3 Ultrahigh-Throughput Screening Assays -- 8.6 Forthcoming Trends in Directed Evolution -- 8.7 Concluding Remarks -- Acknowledgments -- Abbreviations -- References -- 9 Insights into the Structure and Molecular Mechanisms of -Lactam Synthesizing Enzymes in Fungi -- 9.1 Introduction -- 9.1.1 Penicillin and Cephalosporin Biosynthesis: A Brief Overview -- 9.1.2 Genes Involved in Penicillin Biosynthesis -- 9.2 ACV Synthetase -- 9.2.1 The ACV Assembly Line -- 9.2.2 The Cleavage Function of the Integrated Thioesterase Domain -- 9.2.3 The Quality Control (Proofreading) Role of the Thioesterase Domain -- 9.2.4 ACV Analog Dipeptides and Tripeptides Synthesized by the ACVS in Vitro -- 9.3 Isopenicillin N Synthase -- 9.3.1 Binding and Lack of Cyclization of the LLL-ACV -- 9.3.2 The Iron-Containing Active Center -- 9.3.3 The Crystal Structure of IPNS -- 9.3.4 Oxidase and Oxygenase Activities of IPNS.Elsevie

Chemistry and pharmacology of naturally occurring bioactive compounds / edited by Goutam Brahmachari.

562 p. :Natural products play crucial roles in modern drug development, and constitute a prolific source of novel lead compounds or pharmacophores for ongoing drug discovery programs. Chemistry and pharmacology of naturally occurring bioactive compounds presents cutting-edge research in the chemistry of bioactive natural products and demonstrates how natural product research continues to make significant contributions in the discovery and development of new medicinal entities

Sulfamic Acid-Catalyzed One-Pot Room Temperature Synthesis of Biologically Relevant Bis-Lawsone Derivatives

A simple and energy-efficient green protocol for the synthesis of a series of biologically interesting functionalized bis-lawsone [i.e., 3,3′-(aryl/alkyl-methylene)­bis­(2-hydroxynaphthalene-1,4-dione)] scaffolds has been developed in the presence of sulfamic acid as an eco-friendly organocatalyst via one-pot pseudomulticomponent reaction at room temperature. The salient features of the present protocol are mild reaction conditions, good to excellent yields, operational simplicity, energy-efficiency, high atom-economy, eco-friendliness, easy isolation of products and no column chromatographic separation